Single-cell RNA-Seq analysis reveals dynamic trajectories during mouse liver development

Abstract

BackgroundThe differentiation and maturation trajectories of fetal liver stem/progenitor cells (LSPCs) are not fully understood at single-cell resolution, and a priori knowledge of limited biomarkers could restrict trajectory tracking.ResultsWe employed marker-free single-cell RNA-Seq to characterize comprehensive transcriptional profiles of 507 cells randomly selected from seven stages between embryonic day 11.5 and postnatal day 2.5 during mouse liver development, and also 52 Epcam-positive cholangiocytes from postnatal day 3.25 mouse livers. LSPCs in developing mouse livers were identified via marker-free transcriptomic profiling. Single-cell resolution dynamic developmental trajectories of LSPCs exhibited contiguous but discrete genetic control through transcription factors and signaling pathways. The gene expression profiles of cholangiocytes were more close to that of embryonic day 11.5 rather than other later staged LSPCs, cuing the fate decision stage of LSPCs. Our marker-free approach also allows systematic assessment and prediction of isolation biomarkers for LSPCs.ConclusionsOur data provide not only a valuable resource but also novel insights into the fate decision and transcriptional control of self-renewal, differentiation and maturation of LSPCs.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4342-x) contains supplementary material, which is available to authorized users.

Lgr5+ stem/progenitor cells reside at the apex of the embryonic hepatoblast pool

“…We found that the three clusters corresponded to proliferating hepatoblasts (HB), hepatocyte-like progenitors (Hep) and cholangiocyte-like progenitors (Chol), which express higher levels of representative markers. The hepatoblast cluster contained Id3, Mdk and Gpc3, all described as hepatoblast markers (Su et al, 2017; Yang et al, 2017) while the hepatocyte-like cluster presented Ttr, Alb, Apoa1, Apoa2 and C3 all known hepatocyte markers and the cholangiocyte-like cluster expressed the ductal cell genes Car2, Cd44 and Bcl11a (Yang et al, 2017) (Fig. 5B and Supplementary dataset 1_S1-S7).…”

Mutational and transcriptomic landscapes of a rare human prostate basal cell carcinoma

“…Immunohistochemical staining was done as previously described, 24 and we used the following primary antibodies: P63 (ab124762; Abcam), CK34βE12 (M0630; Dako), CK14 (ab7800; Abcam), prostatic acid phosphatase (PAP) (M0792; Dako), and prostate‐specific antigen (PSA) (A056201; Dako). We used biotinylated universal link antibody as the secondary antibody.…”

“…Single‐cell RNA‐Seq experiment and analysis were conducted as previously described 24 . Single‐cell capture, lysis, reverse‐transcription, and complementary DNA amplification were done in a microfluidic‐based C1 RNA‐Seq IFC (10‐17 μm; Fluidigm).…”

“…Single-cell RNA-Seq experiment and analysis were conducted as previously described. 24 Single-cell capture, lysis, reverse-transcription, and complementary DNA amplification were done in a microfluidic-based C1 RNA-Seq IFC (10-17 μm; Fluidigm). After library preparation with Nextera XT Kit and Index Kit (Illumina), the single-cell libraries were pooled and sequenced using NextSeq 500 (Illumina) with 2 × 76 bp sequencing mode.…”

“…Transcription factors (TFs) covariance network analysis was conducted to reveal the relationship of the TFs, specifically expressed in each cell cluster as previously described. 24,32 Gene expression files were retrieved from five other prostate cancer studies 10,11,18,33,34 for comparison studies.…”